modules.pm

#!/usr/bin/perl -w

package modules;

use strict;

# All of the different modules that can be called in the execution of the 
# pipeline are defined here.  Each module needs to know the commands used
# to execute programs as well as information on where the module should look
# for and write data to etc.
sub defineModules {
  @main::bamtoolsList = ("BAMTOOLS",
              "INDEX",
              "RESOLVE",
              "MODIFY_BAM",
              "MERGE_BAM",
              "BAM_STATISTICS"
             );

  foreach (@main::bamtoolsList) {
    $main::modules{"$_"} = {
      BIN              => "/share/software/bamtools/bin",
      COMMAND          => "bamtools",
      RETAIN           => "no"
    };
  }
  $main::modules{"MERGE_BAM"}->{DIR}      = "merged";
  $main::modules{"BAM_STATISTICS"}->{DIR} = "merged";

  $main::modules{"RENAME_BAM"} = {
    RETAIN     => "yes",
    INPUT      => "local",
    OUTPUT     => "local",
    DIR        => "merged",
    COPYONFAIL => "no"
  };

  $main::modules{"FASTQVALIDATOR"} = {
    BIN        => "/share/software/fastQValidator/statgen/src/bin",
    COMMAND    => "fastQValidator",
    RETAIN     => "yes",
    INPUT      => "local",
    OUTPUT     => "node",
    DIR        => "build",
    COPYONFAIL => ""
  };

  $main::modules{"BQ_RECALIBRATION"} = {
    BIN              => "/share/software/GenomeAnalysisToolKit/gatk.clone.July.2011/dist/",
    COMMAND          => "GenomeAnalysisTK.jar",
    RETAIN           => "no",
    INPUT            => "node",
    OUTPUT           => "node",
    DIR              => "bam",
    COPYONFAIL       => "no"
  };

  $main::modules{"DUPLICATE_MARK_PICARD"} = {
    BIN         => "/share/software/picard/picard-tools-1.52",
    PRE_COMMAND => "java -Xmx8g -jar",
    COMMAND     => "MarkDuplicates.jar",
    RETAIN      => "no",
    INPUT       => "local",
    OUTPUT      => "local",
    DIR         => "merged",
    COPYONFAIL  => "no"
  };

  $main::modules{"DUPLICATE_MARK_BCM"} = {
    BIN              => "/share/software/picard/picard-tools-1.52",
    PRE_COMMAND      => "java -classpath",
    COMMAND          => "sam-1.52.jar",
    RETAIN           => "no",
    INPUT            => "local",
    OUTPUT           => "local",
    DIR              => "merged",
    COPYONFAIL       => "no"
  };

  $main::modules{"SAMTOOLS"} = {
    BIN              => "/share/software/samtools/samtools-0.1.16",
    COMMAND          => "samtools",
    RETAIN           => "yes",
    INPUT            => "local",
    OUTPUT           => "node",
    DIR              => "glf",
    COPYONFAIL       => "no"
  };

  $main::modules{"MD5SUM"} = {
    BIN        => "",
    COMMAND    => "md5sum",
    RETAIN     => "yes",
    INPUT      => "local",
    OUTPUT     => "local",
    DIR        => "merged",
    COPYONFAIL => ""
  };

# Now build aligner specific modules.
#
# Mosaik.
  if ($main::aligner eq "mosaik") {

    # Version 1 modules.
    if (! defined $main::mosaikVersion2) {
      $main::modules{"MOSAIKBUILDV1"} = {
        BIN        => "/share/home/wardag/programs/Mosaik/1.1.0005b/1.1.0005b/bin",
        COMMAND    => "MosaikBuild",
        RETAIN     => "no",
        INPUT      => "local",
        OUTPUT     => "node",
        DIR        => "build",
        COPYONFAIL => "no"
      };

      $main::modules{"MOSAIKALIGNERV1"} = {
        BIN        => "/share/home/wardag/programs/Mosaik/1.1.0005b/1.1.0005b/bin",
        COMMAND    => "MosaikAligner",
        RETAIN     => "no",
        INPUT      => "local",
        OUTPUT     => "node",
        DIR        => "aligner",
        COPYONFAIL => "no"
      };

      $main::modules{"MOSAIKSORT"} = {
        BIN        => "/share/home/wardag/programs/Mosaik/1.1.0005b/1.1.0005b/bin",
        COMMAND    => "MosaikSort",
        RETAIN     => "no",
        INPUT      => "node",
        OUTPUT     => "node",
        DIR        => "sort",
        COPYONFAIL => "no"
      };

      $main::modules{"MOSAIKTEXT"} = {
        BIN        => "/share/home/wardag/programs/Mosaik/1.1.0005b/1.1.0005b/bin",
        COMMAND    => "MosaikText",
        RETAIN     => "no",
        INPUT      => "node",
        OUTPUT     => "node",
        DIR        => "bam",
        COPYONFAIL => "no"
      };

    # Mosaik version 2.
    } else {
      $main::modules{"MOSAIKBUILDV2"} = {
        BIN        => "/share/home/wardag/programs/MOSAIK/bin",
        COMMAND    => "MosaikBuild",
        RETAIN     => "no",
        INPUT      => "local",
        OUTPUT     => "node",
        DIR        => "build",
        COPYONFAIL => "no"
      };

      $main::modules{"MOSAIKALIGNERV2"} = {
        BIN        => "/share/home/wardag/programs/MOSAIK/bin", 
        COMMAND    => "MosaikAligner",
        RETAIN     => "no",
        INPUT      => "local",
        OUTPUT     => "node",
        DIR        => "aligner",
        COPYONFAIL => "no"
      };

      $main::modules{"SORT_MOSAIKV2"} = {
        RETAIN     => "yes",
        INPUT      => "node",
        OUTPUT     => "node",
        DIR        => "bam",
        COPYONFAIL => "yes"
      };
    }

  # BWA.
  } elsif ($main::Aligner =~ /bwa/i) {

  # No aligner.
  } elsif ($main::Aligner =~ /none/i) {
  } else {
    command_line::checkAligner();
  }

  # Now build SNP caller specific modules.  Start with freeBayes.
  $main::modules{"FREEBAYES"} = {
    BIN        => "/share/home/wardag/programs/freebayes/bin",
    COMMAND    => "freebayes",
    RETAIN     => "yes",
    INPUT      => "local",
    OUTPUT     => "local",
    DIR        => "freebayes",
    COPYONFAIL => "no"
  };

  # BamLeftAlign
  $main::modules{"BAM_LEFT_ALIGN"} = {
    BIN        => "/share/home/wardag/programs/freebayes/bin",
    COMMAND    => "bamleftalign",
    RETAIN     => "yes",
    INPUT      => "local",
    OUTPUT     => "local",
    DIR        => "freebayes",
    COPYONFAIL => "no"
  };

  # Ogap
  $main::modules{"OGAP"} = {
    BIN        => "/share/home/wardag/programs/ogap",
    COMMAND    => "ogap",
    RETAIN     => "yes",
    INPUT      => "local",
    OUTPUT     => "local",
    DIR        => "freebayes",
    COPYONFAIL => "no"
  };

}

# Read in the paths of the software components from the supplied file (if
# necessary).
sub readSoftware() {
  my @array;
  my ($tool, $path);
  my (%allowedTools, %allowedFiles);

  # Define a list of allowed tools and files.
  %allowedTools = ('BAM_LEFT_ALIGN', 1,
                   'BAMTOOLS', 1,
                   'DUPBCM', 1,
                   'DUPPICARD', 1,
                   'FASTQVALIDATOR', 1,
                   'FREEBAYES', 1,
                   'GATK', 1,
                   'MOSAIK', 1,
                   'MOSAIK2', 1,
                   'OGAP', 1,
                   'PICARD', 1,
                   'SAMTOOLS', 1);

  # Now include the allowed files.
  %allowedFiles = ('DBSNP', 1,
                   'REF', 1);

  if (defined $main::softwareList && $main::softwareList ne "help") {
    open(SOFTWARE, "<$main::softwareList") || die("Failed to open file: $main::softwareList");
    while(<SOFTWARE>) {
      chomp;
      if (/\S+:\S+/) {
        @array = split(/:/, $_);
        $tool = $array[0];
        $path = $array[1];

        # Check that the tool is allowed.
        if (!exists $allowedTools{$tool} && !exists $allowedFiles{$tool}) {softwareHelp(\%allowedTools, \%allowedFiles);}

        # Strip off trailing /, if exists.
        if ($path =~ /\/$/) {$path = substr($path, 0, -1);}

        # Update the tool with the path given here.
        if ($tool eq "BAMTOOLS") {
          foreach (@main::bamtoolsList) {$main::modules{$_}->{BIN} = $path;}
        } elsif ($tool =~ /^DBSNP$/) {
          $main::dbsnp    = $path;
          $main::dbsnpBin = $path;
          $main::dbsnp    = (split(/\//, $main::dbsnp))[-1];
          $main::dbsnpBin =~ s/\/$main::dbsnp//;
        } elsif ($tool =~ /^REF$/) {
          $main::reference = $path;
        } elsif ($tool eq "DUPBCM") {

          # The path name for picard should include the version number.  Extract
          # this and set the command to sam.version.jar.
          (my $picardVersion = (split(/\//, $path))[-1]) =~ /\s*-(\d+)\.(\d+)/;
          my $major = $1;
          my $minor = $2;
          $main::modules{"DUPLICATE_MARK_BCM"}->{BIN}     = $path;
          $main::modules{"DUPLICATE_MARK_BCM"}->{COMMAND} = "sam-$major.$minor.jar";
        } elsif ($tool eq "DUPPICARD") {
          $main::modules{"DUPLICATE_MARK_PICARD"}->{BIN}  = $path;
        } elsif ($tool eq "GATK") {
          $main::modules{"BQ_RECALIBRATION"}->{BIN}       = $path;
        } elsif ($tool eq "MOSAIK") {
          $main::modules{"MOSAIKBUILDV1"}->{BIN}          = $path;
          $main::modules{"MOSAIKALIGNERV1"}->{BIN}        = $path;
          $main::modules{"MOSAIKSORT"}->{BIN}             = $path;
          $main::modules{"MOSAIKTEXT"}->{BIN}             = $path;
        } elsif ($tool eq "MOSAIK2") {
          $main::modules{"MOSAIKBUILDV2"}->{BIN}          = $path;
          $main::modules{"MOSAIKALIGNERV2"}->{BIN}        = $path;
        } else {
          $main::modules{$tool}->{BIN} = $path;
        }
      } else {
        softwareHelp(\%allowedTools, \%allowedFiles);
      }
    }
  } elsif (defined $main::softwareList && $main::softwareList eq "help") {
    softwareHelp(\%allowedTools, \%allowedFiles);
  }
}

#
sub softwareHelp {
  my %allowedTools = %{$_[0]};
  my %allowedFiles = %{$_[1]};

  print STDERR ("\n***SCRIPT TERMINATED***\n\n");
  print STDERR ("Incorrect format in string.  Entries must be of the form:\n");
  print STDERR ("\t<TOOL>:<PATH>\n");
  print STDERR ("\t<FILENAME>:<PATH>/<FILE>\n\n");
  print STDERR ("Allowed tools include:\n");
  foreach my $key (keys %allowedTools) {print STDERR ("\t$key\n");}
  print STDERR ("\n");
  print STDERR ("Allowed files include:\n");
  foreach my $key (keys %allowedFiles) {print STDERR ("\t$key\n");}
  print("\n");
  print STDERR ("Error in modules::readSoftware.\n");
  exit(1);
}

1;